rs4784549

Positions:

• chr16-55579006-T-A
• chr16-55579006-T-C
• chr16-55579006-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017839.5(LPCAT2):​c.1315-103T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 1,053,600 control chromosomes in the GnomAD database, including 165,492 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (29231 hom., cov: 32)
  • Exomes 𝑓: 0.54 (136261 hom.)
• Consequence: LPCAT2 NM_017839.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

Genes affected

LPCAT2 (HGNC:26032): (lysophosphatidylcholine acyltransferase 2) This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPCAT2	NM_017839.5	c.1315-103T>A		intron_variant		ENST00000262134.10	NP_060309.2
LPCAT2	XM_011523169.4	c.505-103T>A		intron_variant			XP_011521471.1
LPCAT2	XM_047434277.1	c.1147-103T>A		intron_variant			XP_047290233.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPCAT2	ENST00000262134.10	c.1315-103T>A		intron_variant		1	NM_017839.5	ENSP00000262134	P1
LPCAT2	ENST00000566915.5	n.1397-103T>A		intron_variant, non_coding_transcript_variant		1
LPCAT2	ENST00000565056.1	n.189-103T>A		intron_variant, non_coding_transcript_variant		3
LPCAT2	ENST00000562299.1			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92111 AN: 152002 Hom.: 29194 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.543 AC: 489942 AN: 901480 Hom.: 136261 Cov.: 12 AF XY: 0.547 AC XY: 253023 AN XY: 462238

Gnomad4 AFR exome AF: 0.805

Gnomad4 AMR exome AF: 0.559

Gnomad4 ASJ exome AF: 0.488

Gnomad4 EAS exome AF: 0.719

Gnomad4 SAS exome AF: 0.687

Gnomad4 FIN exome AF: 0.521

Gnomad4 NFE exome AF: 0.512

Gnomad4 OTH exome AF: 0.559

GnomAD4 genome AF: 0.606 AC: 92203 AN: 152120 Hom.: 29231 Cov.: 32 AF XY: 0.609 AC XY: 45302 AN XY: 74360

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.589

Alfa AF: 0.559 Hom.: 3019

Bravo AF: 0.614

Asia WGS AF: 0.775 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.045
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4784549; hg19: chr16-55612918; COSMIC: COSV50896865; COSMIC: COSV50896865;